Difference between revisions of "WormBase-Caltech Weekly Calls"
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Human diseases will be objectified | Human diseases will be objectified | ||
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+ | == February 23, 2012 == | ||
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+ | BioCurator Meeting | ||
+ | *Karen, Arun, Kimberly, Michael and Yuling are going | ||
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+ | GO Consortium meeting this weekend |
Revision as of 19:04, 23 February 2012
Contents
2012 Meetings
February 2, 2012
EPIC data into WormBase
- Daniela spoke to John Murray
- Need to modify model and display for data
- 3D movies as ?Movie objects
Endrov
- Tom Burglin and student Johan Henriksson developed Endrov.net (http://www.endrov.net)
- May be able to incorporate Endrov visualizations of Blender model and cell lineage into WormBase website?
- Need to talk to Todd and Web team
Elsevier legal issues
- Science-direct website links to-and-from WormBase website
- Daniela still working with contacts at MGI (Mouse Genomics Institute/Jackson Labs) & Elsevier
- MGI already has established links with Elsevier
New ?Interaction model
- Update old objects and speak to web team about new model before officially incorporating new ?Interaction model
February 9, 2012
Interaction model
- Added some XREFs (in Interactor tag) and Chromatin_IP to Detection method
- Co-Immunoprecipitation would be captured under Detection method "Affinity Capture Western"
- Worked out changes needed for old *.ACE files to fit new model; will give to Juancarlos to script
Transgene
- Daniela, Juancarlos, and Karen imported Extrachromosomal array transgenes into the Transgene OA
- Extrachromosomal array transgenes for which authors have not provided a name will be named Expr####_Ex
- Maybe we will name according to paper e.g. "WBPaper########_Ex####"
- Daniela and Karen will discuss cost-benefit of objectifying Ex transgenes
- Rather than determine transgene sequence (or partial sequence), curators will (as they have been for Expr_pattern) add free-text describing the sequence
- This includes: primer sets, restriction digest sites, etc.
- Continue to place this info in the Reporter_gene tag
- Maybe add an additional free-text field (Sequence_info tag?)
Displaying curator names on new website
- Should we display curators' names on their curated objects?
- Currently only on concise description; why not do all objects?
- Keep curator name info only internal?
- Prevent curator names from being dumped for build/release?
- Should include 'Date-last-updated' Evidence dump
- Curator confirmed note could be placed in Tree View for all data types
Incremental Updates
- Should we perform incremental updates?
- Update as frequently as possible?
- Web display (of updates) served from Postgres/Tazendra?
- Serve RESTful widget from Caltech?
- Caltech in agreement about pushing forward with incremental updates
February 16, 2012
Gene product annotation for variation
- Variation affects gene product: absent, disfunctional, isoform-specific effects
- How is this best captured?
- Report as a phenotype? "RNA expression variant", "protein expression variant", etc...
- Capture as a gene_regulation event? Soon will be interaction object...
- Sequence ontology?
- Captured in ?Variation?
- Ask Hinxton/Mary Ann Tuli
Interaction model
- Old objects updated OK and read into ACEDB without problems
- Need to discuss updates with Web team
- Will send all updated *.ACE files with old Gene_regulaion, Interaction, and YH objects
- Add two zeros to the Interaction IDs in postgres OA tables once all current interaction objects uploaded to the Interaction OA
Transgene naming
- New extrachromosomal arrays will get "WBPaper###_Ex###" type of ID
SPELL Issues
- Problems coming up as data size increasing
- SPELL server at Amazon running at lowest paid instance ($1000/yr)
- 4GB memory needed (more than 132-bit machine can provide) for loading data
- 64-bit machine will cost $4000 per year
- Run SPELL on canopus? Yes but, have to take care of sys-admin issues
- $500/quarter for IMSS machine maintenance
- Talk to Matt Hibbs? Maybe need to optimize the process at that step
BioCreative/BioCurator meetings
- Kimberly working with DictyBase
- Kimberly will give 2 talks (CCC and molecular function automated curation)
- WormBase workflow; Kimberly will discuss with individual curators in March
- Arun submitted abstract
GO Consotrium meeting in a week and a half
- Paul, Michael (Muller) and Kimberly going
Human diseases will be objectified
February 23, 2012
BioCurator Meeting
- Karen, Arun, Kimberly, Michael and Yuling are going
GO Consortium meeting this weekend